Topic 6 Flashcards
Mutations in which organ has the greatest evolutionary effect?
the gonads
What are the two types of mutations?
Germinal: only mutations in the germ cells will be transmitted to the progeny
Somatic mutations: will impact the individual where the mutation occurs but are evolutionarily irrelevant
What is the reigning paradigm of mutations?
Mutations can occur in any cell at any time, and their occurrence is ‘random’.
True or false? Mutagenic processes are at a constant tug-of-war with eachother.
True
DNA is a remarkably stable molecule, but it can still be damaged due to chemical or physical stress on the double helix.
What are the five types of damage?
(1) Abasic sites (loss of nucleotide, not backbone)
(2) Base mismatches
(3) Modified bases
(4) Inter- and intra-strand crosslinks
(5) Double stranded breaks (DSBs)
What is the range of genetic mutations?
Causes everything from point mutation (1bp affected) to structural changes affecting the whole chromosomes (deletions, inversions, duplications, translocations)
Compare spontaneous and induced mutations.
spontaneous mutations are mostly from replication errors (polymerase-induced mistakes) followed by defects in the DNA repair mechanism. The rate of spontaneous mutations is very low and varies according to gene size, domains on the chromosome, genome characteristics, and cell age.
Induced mutations (known as chemical and physical agents or mutagens) have a higher frequency and include base analogs, hydroxylating agents, alkylating agents, deaminating agents, intercalating agents, UV radiation, and ionizing radiation.
What are point mutations and where do they take place?
Single base pair changes or single nucleotide polymorphism (SNP) that can occur anywhere in the genome (coding regions, intergenic regions, non-coding regions of genes like promoters, UTRs, or introns)
What are the three types of point mutations?
(1) Base substitutions
(2) Base deletion
(3) Base insertion
What are the kinds of base substitution point mutations?
Transition:
purine replaced by a purine (A-G, G-A)
pyrimidine replaced by a pyrimidine (C-T, T-C)
Transversion:
purine replaced by a pyrimidine (A-C, A-T, G-C, G-T)
Pyrimidine replaced by a purine (C-A, C-G, T-A, T-G)
Name synonymous and non-synonymous mutations.
Synonymous:
Silent mutations- encodes the same amino acid, usually in the third degenerate position, with no effect on the phenotype
Non-synonymous:
Missense Mutations- codes for a different amino acid
Nonsense mutations- changes to a STOP codon, likely severe
What will cause for a missense mutation to either retain protein function or not?
Chemically similar– conservative, may retain protein function
Chemically different– non-conservative, more likely to affect protein function
Describe a frameshift mutation.
Removal or addition of base pairs disrupts the triplet reading frame.
The result is the translation of an abnormal series of aa downstream from the indel and the increased chances of a premature STOP codon producing a truncated protein.
Indels (insertions/deletions) that are multiple of three reconstitute the frame downstream of the last mutation site
Explain functional consequences of mutations in the non-coding regions of DNA.
Point mutations in regulatory regions required for gene expression (promoters, enhancers, etc.) or that are involved in mRNA processing and stability (splice sites, UTRs) may ultimately affect how much protein is made
A mutation in the Shine-Delgarno sequence will effect
(a) Prokaryotic transcription
(b) Eukaryotic transcription
(c) Prokaryotic translation
(d) Eukaryotic translation
(e) none of the above
Prokaryotic translation
This ribosomal binding site in bacterial messenger RNA became known as the Shine-Dalgarno (SD) sequence enables initiation of protein synthesis by aligning the ribosome with the start codon.
What mutation is caused by error in replication?
DNA slippage causes indels during replication– usually of repeated regions
What does slippage mutations result in?
The daughter strand gets looped and that part of the template is repeated
What is the result of CGG expansion in Fragile X syndrome?
The methylation of 5’ regulatory sequences and transcription silencing
Note: slippage is behind an important class of mutations defined by trinucleotide repeats that explains over 40 inherited neurological diseases such as Fragile X syndrome (CGG repeats in the FMR1 gene) and Huntington Disease (CAG repeats in the huntington gene)
How do you determine if a chemical is a mutagen or carcinogen?
The frequency of mutant animals that can survive after exposure to a mutagen reflects the number of times the reversion mutation occurred in the same position in the same gene because of exposure to a mutagen. This frequency is a measure of mutagenic potential of mutagens.
How do you determine Mutagenicity Ratio (MR)?
MR = total number of revertants / number of spontaneous revertants
The control plate shows spontaneous mutation rate
The test plate displays the total (spontaneous + induced mutation rate)
Autosomal recessive
Parents are AA and aa
because mutant is recessive to one parent is guaranteed to be homozygous recessive and the mutation is rare so we assume the other parent is homozygous dominant.
100% probability that V-1 is heterozygous
DNA repair mechanisms overview
Translation synthesis was not covered
Four main types: base excision repair, nucleotide excision repair, mismatch repair, and nonhomologous end joining.
Simplest is basic excision repair: one of the bases has a small modification to it, fairly simple repair because the repair mechanism can know the correct base
More serious/awkward damage: nucleotide excision repair, takes out the whole nucleotide including the backbone, or a bulky adduct.
Likely happening with DNA polymerase: mismatch repair, proteins and functions in the polymerase itself
Most serious: double stranded breaks, two ways of repair, the best is HR but also uses NHEJ, broken DNA ends erode quickly so this is an emergency repair
Compare homologous recombination and non-homologous end joining DBS repair
Do not need to know the complex steps and all the details, just know how HR is different from NHEJ
Describe homologous recombination DBS repair.
Note: requires an undamaged template from a sister chromatid or homologous chromosome
(1) Detection
(2) Strand Resection
Creates 3’ overhands (sticky ends) required for strand exchange
(3) Strand exchange/invasion
3’ overhang invades template strands
recombinase mediated
Forms a D-loop (displacement loop)
(4) Polymerization
Using the homolog/sister as template, the invading strand is extended by polymerases
These intermediates can be either processed by:
Synthesis dependent strand annealing pathway (SDSA)
Double strand break repair pathway (BSBR)
The intermediates of homologous recombination DBS repair can then be processed by either
(1) Synthesis Dependent Strand Annealing Pathway (SDSA)
(2) Double Strand Break Repair Pathway (DSBR)
Describe the first.
DNA helicases break invading off the homologous template after polymerization and original strands re-anneal.
Gaps are filled by DNA polymerase and strands reconnected by DNA ligase
There is no chance of strand exchange in this scenario.
The intermediates of homologous recombination DBS repair can then be processed by either
(1) Synthesis Dependent Strand Annealing Pathway (SDSA)
(2) Double Strand Break Repair Pathway (DSBR)
Describe the second.
(1) Second strand invades, associates with template
This forms a two crossover intermediate structure referred as a double Holliday Junctions
(2) Resolution of intermediates
Endonucleases cleave HJs to release recombined or non-recombined products
(3) Polymerization and ligation
Polymerases fill gaps between the strands and DNA ligases connect the cleaved strands
